April 11th, 2017
Finak, Frelinger, Jiang, et al. (2014)
The two top performing gating algorithms - OpenCyto (v. 1.7.4), flowDensity (v. 1.4.0) - in a study run by the FlowCAP consortium aimed at selecting the best performing algorithms for this larger study were chosen for the analysis presented in this paper. Standardizing Flow Cytometry Immunophenotyping Analysis from the Human ImmunoPhenotyping Consortium Finak, Langweiler, Jaimes, et al. (2016)
| N_SAMPS | N_DATA | RHO | BETA | BETA_SE | R2 | ICC_1 |
|---|---|---|---|---|---|---|
| 151 | 2265 | 0.9846 | 1.015 | 0.0015 | 0.9949 | 0.9972 |
| N_SAMPS | N_DATA | RHO | BETA | BETA_SE | R2 | ICC_1 |
|---|---|---|---|---|---|---|
| 151 | 2265 | 0.979 | 0.9861 | 0.0031 | 0.9782 | 0.989 |
| FN | TN | TP | FP | ACC | SENS | SPEC | PREC | |
|---|---|---|---|---|---|---|---|---|
| Freq | 1490 | 142572 | 28420 | 0 | 0.9914 | 0.9502 | 1 | 1 |
| FN | FP | TN | TP | ACC | SENS | SPEC | PREC | |
|---|---|---|---|---|---|---|---|---|
| Freq | 2849 | 22579 | 778949 | 38211 | 0.9698 | 0.9306 | 0.9718 | 0.6286 |
| N_SAMPS | N_DATA | RHO | BETA | BETA_SE | R2 | ICC_1 |
|---|---|---|---|---|---|---|
| 151 | 151 | 0.9885 | 1.014 | 0.0078 | 0.9912 | 0.9953 |
| N_SAMPS | N_DATA | RHO | BETA | BETA_SE | R2 | ICC_1 |
|---|---|---|---|---|---|---|
| 151 | 151 | 0.9968 | 1.038 | 0.005 | 0.9966 | 0.9972 |
| FN | FP | TN | TP | ACC | SENS | SPEC | PREC | |
|---|---|---|---|---|---|---|---|---|
| Freq | 224 | 10743 | 1096246 | 84062 | 0.9908 | 0.9973 | 0.9903 | 0.8867 |
| FN | FP | TN | TP | ACC | SENS | SPEC | PREC | |
|---|---|---|---|---|---|---|---|---|
| Freq | 10397 | 46 | 1237576 | 143142 | 0.9925 | 0.9323 | 1 | 0.9997 |
| N_SAMPS | N_DATA | RHO | BETA | BETA_SE | R2 | ICC_1 |
|---|---|---|---|---|---|---|
| 151 | 151 | 0.9822 | 1.018 | 0.0087 | 0.9892 | 0.9935 |
| N_SAMPS | N_DATA | RHO | BETA | BETA_SE | R2 | ICC_1 |
|---|---|---|---|---|---|---|
| 151 | 151 | 0.0585 | 0.032 | 0.0225 | 0.0134 | -0.0278 |
| FN | FP | TN | TP | ACC | SENS | SPEC | PREC | |
|---|---|---|---|---|---|---|---|---|
| Freq | 213 | 10668 | 1096940 | 83454 | 0.9909 | 0.9975 | 0.9904 | 0.8867 |
| FN | FP | TN | TP | ACC | SENS | SPEC | PREC | |
|---|---|---|---|---|---|---|---|---|
| Freq | 17050 | 7378 | 476522 | 178534 | 0.964 | 0.9128 | 0.9848 | 0.9603 |
| N_SAMPS | N_DATA | RHO | BETA | BETA_SE | R2 | ICC_1 |
|---|---|---|---|---|---|---|
| 151 | 151 | 0.9821 | 1.019 | 0.0088 | 0.9889 | 0.9933 |
| N_SAMPS | N_DATA | RHO | BETA | BETA_SE | R2 | ICC_1 |
|---|---|---|---|---|---|---|
| 151 | 151 | 0.6801 | 1.064 | 0.0931 | 0.4672 | 0.6227 |
| FN | FP | TN | TP | ACC | SENS | SPEC | PREC | |
|---|---|---|---|---|---|---|---|---|
| Freq | 4244 | 273 | 1454088 | 136130 | 0.9972 | 0.9698 | 0.9998 | 0.998 |
| FN | FP | TN | TP | ACC | SENS | SPEC | PREC | |
|---|---|---|---|---|---|---|---|---|
| Freq | 1393 | 3028 | 603276 | 43658 | 0.9932 | 0.9691 | 0.995 | 0.9351 |
| N_SAMPS | N_DATA | RHO | BETA | BETA_SE | R2 | ICC_1 |
|---|---|---|---|---|---|---|
| 151 | 151 | 0.9958 | 0.9979 | 0.0054 | 0.9956 | 0.9978 |
| N_SAMPS | N_DATA | RHO | BETA | BETA_SE | R2 | ICC_1 |
|---|---|---|---|---|---|---|
| 151 | 151 | 0.9784 | 0.9059 | 0.0133 | 0.9687 | 0.9711 |
| FN | FP | TN | TP | ACC | SENS | SPEC | PREC | |
|---|---|---|---|---|---|---|---|---|
| Freq | 880 | 104 | 524259 | 6874 | 0.9982 | 0.8865 | 0.9998 | 0.9851 |
| FN | FP | TN | TP | ACC | SENS | SPEC | PREC | |
|---|---|---|---|---|---|---|---|---|
| Freq | 5807 | 7577 | 963616 | 94294 | 0.9875 | 0.942 | 0.9922 | 0.9256 |
| N_SAMPS | N_DATA | RHO | BETA | BETA_SE | R2 | ICC_1 |
|---|---|---|---|---|---|---|
| 151 | 151 | 0.9891 | 1.015 | 0.0113 | 0.982 | 0.9897 |
| N_SAMPS | N_DATA | RHO | BETA | BETA_SE | R2 | ICC_1 |
|---|---|---|---|---|---|---|
| 151 | 151 | 0.9709 | 0.9173 | 0.0215 | 0.9241 | 0.9539 |
| N_SAMPS | N_DATA | RHO | BETA | BETA_SE | R2 | ICC_1 |
|---|---|---|---|---|---|---|
| 151 | 151 | 0.9643 | 0.9344 | 0.0238 | 0.9121 | 0.9542 |
| N_SAMPS | N_DATA | RHO | BETA | BETA_SE | R2 | ICC_1 |
|---|---|---|---|---|---|---|
| 151 | 151 | 0.898 | 0.7929 | 0.0329 | 0.7959 | 0.8867 |
| FN | FP | TN | TP | ACC | SENS | SPEC | PREC | |
|---|---|---|---|---|---|---|---|---|
| Freq | 3307 | 1114 | 2113444 | 22741 | 0.9979 | 0.873 | 0.9995 | 0.9533 |
| FN | FP | TN | TP | ACC | SENS | SPEC | PREC | |
|---|---|---|---|---|---|---|---|---|
| Freq | 953 | 19155 | 786225 | 21460 | 0.9757 | 0.9575 | 0.9762 | 0.5284 |
| N_SAMPS | N_DATA | RHO | BETA | BETA_SE | R2 | ICC_1 |
|---|---|---|---|---|---|---|
| 151 | 151 | 0.7592 | 0.8319 | 0.0386 | 0.7567 | 0.8635 |
| N_SAMPS | N_DATA | RHO | BETA | BETA_SE | R2 | ICC_1 |
|---|---|---|---|---|---|---|
| 151 | 151 | 0.7198 | 0.7991 | 0.0695 | 0.47 | 0.661 |
| FN | FP | TN | TP | ACC | SENS | SPEC | PREC | |
|---|---|---|---|---|---|---|---|---|
| Freq | 1509 | 240 | 1382591 | 6821 | 0.9987 | 0.8188 | 0.9998 | 0.966 |
| FN | FP | TN | TP | ACC | SENS | SPEC | PREC | |
|---|---|---|---|---|---|---|---|---|
| Freq | 974 | 6718 | 948445 | 12272 | 0.9921 | 0.9265 | 0.993 | 0.6462 |
| N_SAMPS | N_DATA | RHO | BETA | BETA_SE | R2 | ICC_1 |
|---|---|---|---|---|---|---|
| 151 | 151 | 0.8323 | 0.7918 | 0.0357 | 0.7677 | 0.8681 |
| N_SAMPS | N_DATA | RHO | BETA | BETA_SE | R2 | ICC_1 |
|---|---|---|---|---|---|---|
| 151 | 151 | 0.7935 | 0.7057 | 0.0462 | 0.6104 | 0.7736 |
| FN | FP | TN | TP | ACC | SENS | SPEC | PREC | |
|---|---|---|---|---|---|---|---|---|
| Freq | 827 | 244 | 926060 | 26892 | 0.9989 | 0.9702 | 0.9997 | 0.991 |
| FN | FP | TN | TP | ACC | SENS | SPEC | PREC | |
|---|---|---|---|---|---|---|---|---|
| Freq | 18678 | 251 | 789709 | 19155 | 0.9771 | 0.5063 | 0.9997 | 0.9871 |
| N_SAMPS | N_DATA | RHO | BETA | BETA_SE | R2 | ICC_1 |
|---|---|---|---|---|---|---|
| 151 | 151 | 0.9714 | 0.9777 | 0.0133 | 0.9733 | 0.9853 |
| N_SAMPS | N_DATA | RHO | BETA | BETA_SE | R2 | ICC_1 |
|---|---|---|---|---|---|---|
| 151 | 151 | 0.9394 | 0.7853 | 0.0327 | 0.7947 | 0.885 |
| FN | FP | TN | TP | ACC | SENS | SPEC | PREC | |
|---|---|---|---|---|---|---|---|---|
| Freq | 2478 | 2311 | 1665944 | 30763 | 0.9972 | 0.9255 | 0.9986 | 0.9301 |
| FN | FP | TN | TP | ACC | SENS | SPEC | PREC | |
|---|---|---|---|---|---|---|---|---|
| Freq | 2892 | 5308 | 926823 | 33386 | 0.9915 | 0.9203 | 0.9943 | 0.8628 |
| N_SAMPS | N_DATA | RHO | BETA | BETA_SE | R2 | ICC_1 |
|---|---|---|---|---|---|---|
| 151 | 151 | 0.9485 | 0.9527 | 0.0259 | 0.9011 | 0.9493 |
| N_SAMPS | N_DATA | RHO | BETA | BETA_SE | R2 | ICC_1 |
|---|---|---|---|---|---|---|
| 151 | 151 | 0.9343 | 0.9315 | 0.0324 | 0.847 | 0.9204 |
| FN | FP | TN | TP | ACC | SENS | SPEC | PREC | |
|---|---|---|---|---|---|---|---|---|
| Freq | 531 | 895 | 937430 | 15167 | 0.9985 | 0.9662 | 0.999 | 0.9443 |

| FN | FP | TN | TP | ACC | SENS | SPEC | PREC | |
|---|---|---|---|---|---|---|---|---|
| Freq | 521 | 8506 | 2738594 | 23528 | 0.9967 | 0.9783 | 0.9969 | 0.7345 |
| N_SAMPS | N_DATA | RHO | BETA | BETA_SE | R2 | ICC_1 |
|---|---|---|---|---|---|---|
| 151 | 151 | 0.9377 | 0.9254 | 0.0296 | 0.8679 | 0.9262 |
| N_SAMPS | N_DATA | RHO | BETA | BETA_SE | R2 | ICC_1 |
|---|---|---|---|---|---|---|
| 151 | 151 | 0.8809 | 1.002 | 0.0428 | 0.7857 | 0.8714 |
| N_SAMPS | N_DATA | RHO | BETA | BETA_SE | R2 | ICC_1 |
|---|---|---|---|---|---|---|
| 151 | 151 | 0.909 | 0.8173 | 0.0403 | 0.7344 | 0.8424 |
| N_SAMPS | N_DATA | RHO | BETA | BETA_SE | R2 | ICC_1 |
|---|---|---|---|---|---|---|
| 151 | 151 | 0.9128 | 0.8498 | 0.0367 | 0.7828 | 0.868 |
| N_SAMPS | N_DATA | RHO | BETA | BETA_SE | R2 | ICC_1 |
|---|---|---|---|---|---|---|
| 151 | 151 | 0.823 | 1.16 | 0.0443 | 0.8211 | 0.8764 |
| N_SAMPS | N_DATA | RHO | BETA | BETA_SE | R2 | ICC_1 |
|---|---|---|---|---|---|---|
| 151 | 151 | 0.8057 | 0.4608 | 0.0449 | 0.4145 | 0.5765 |
| N_SAMPS | N_DATA | RHO | BETA | BETA_SE | R2 | ICC_1 |
|---|---|---|---|---|---|---|
| 151 | 151 | 0.9212 | 0.7128 | 0.0113 | 0.964 | 0.925 |
| N_SAMPS | N_DATA | RHO | BETA | BETA_SE | R2 | ICC_1 |
|---|---|---|---|---|---|---|
| 151 | 151 | 0.8844 | 0.7361 | 0.0349 | 0.7487 | 0.8423 |
Tested FlowAI
… consists of three key steps to check and remove suspected anomalies that derive from (i) abrupt changes in the flow rate, (ii) instability of signal acquisition and (iii) outliers in the lower limit and margin events in the upper limit of the dynamic range. flowAI: automatic and interactive anomaly discerning tools for flow cytometry data. Monaco, Chen, Poidinger, et al. (2016)
From Wikipedia
Cicchetti (1994) gives the following often quoted guidelines for interpretation for kappa or ICC inter-rater agreement measures: